Covid-dash

COVID-19 European news text analysis dashboard for the Embeddia hackathon.

Ingress + analysis pipeline

Manual setup

$ curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -

Or in Powershell:

$ (Invoke-WebRequest -Uri https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py -UseBasicParsing).Content | python -

Install:

$ ./install.sh

If you want to run the usenews extraction you also need to install R, including development packages (r-base and r-base-dev on Debian-oids) and the usenews extra:

$ ./install.sh -E usenews

Docker/Singularity

Containers use GitHub Container Registry.

Pull with Docker:

$ docker pull ghcr.io/mood-mapping-muppets/pipe:latest

Pull with Singularity:

$ singularity pull docker://ghcr.io/mood-mapping-muppets/pipe:latest

Running ingress

Manually you can run:

$ cd ingress
$ poetry run snakemake get_covid_march

On CSC you first need to get singslurm2:

$ cd /projappl/project_2003933
$ git clone --recursive https://github.com/frankier/singslurm2.git

You can then copy the files in contrib/csc into a working directory and modify the paths as necessary and then run:

$ nohup ./run.sh &

Note you CWD must not contain any symlinks when running Singularity. To be safe you should run e.g. cd $(realpath .) first.

Dashboard

Manual setup and run

Get Poetry as above.

Change directory and install.

$ cd dashboard
$ poetry install

Now you can run:

$ poetry run python app.py

Docker

You can run the production Dockerfile locally.

$ docker run ghcr.io/mood-mapping-muppets/web:latest

Deploying to Rahti

The container is automatically deployed through GitHub actions.

mood-mapping-muppets/repo